Analysis module 4: 16S vs ORV outcome RoVI study — 31 October, 2022

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Sample summary

Alpha diversity

Beta diversity

Differential taxa

Summary figures

Longitudinal abundance comparisons

Session info

Sample summary

Input data: infant stools (BS1, BS2, BS3, and BS5) and maternal stool (MS1)

  • n samples = 2086
  • n taxa: genera = 502; variants = 6372
  • n taxa (rarefied): genera = 472; variants = 6235

Statistical methods for mixed-effects models

  • Linear mixed-effects models fit with family ID as a random effect
  • Association with ORV outcome determined by comparing fit of model with country/age vs model with age alone

Alpha diversity

Column

Seroconversion

Longitudinal plots - Shannon

Longitudinal plots - richness

Longitudinal plots - E/B ratio

Blue = seroconversion+, Orange = seroconversion-.

P values - E/B ratio

IND

    Wilcoxon rank sum test with continuity correction

data:  log_Entero_Bac_ratio by seroconv
W = 8673.5, p-value = 0.4668
alternative hypothesis: true location shift is not equal to 0
MLW

    Wilcoxon rank sum test with continuity correction

data:  log_Entero_Bac_ratio by seroconv
W = 230, p-value = 0.1201
alternative hypothesis: true location shift is not equal to 0
UK

    Wilcoxon rank sum exact test

data:  log_Entero_Bac_ratio by seroconv
W = 334, p-value = 0.3457
alternative hypothesis: true location shift is not equal to 0
IND neo+

    Wilcoxon rank sum test with continuity correction

data:  log_Entero_Bac_ratio by seroconv
W = 2956, p-value = 0.0627
alternative hypothesis: true location shift is not equal to 0
IND neo-

    Wilcoxon rank sum test with continuity correction

data:  log_Entero_Bac_ratio by seroconv
W = 1466.5, p-value = 0.3816
alternative hypothesis: true location shift is not equal to 0

N by country

, ,  = IND

   
    BS1 BS2 BS3 BS5
  0 208 209 208 202
  1  79  76  79  79

, ,  = MLW

   
    BS1 BS2 BS3 BS5
  0  55  56  54  44
  1  18  15  12   9

, ,  = UK

   
    BS1 BS2 BS3 BS5
  0  23  24  23  24
  1  27  26  25  25

, ,  = IND (neo+)

   
    BS1 BS2 BS3 BS5
  0 108 110 108 111
  1  47  46  46  49

, ,  = IND (neo-)

   
    BS1 BS2 BS3 BS5
  0  99  98  99  90
  1  32  30  33  30

P values, cross-sectional analayses

See Module 5 for full univariate and multivariate analyses.

P values, longitudinal mixed-effects models

           Shannon log(Observed)
IND         0.0101        0.0018
IND (neo+)  0.3252        0.3407
IND (neo-)  0.0035        0.0002
MLW         0.5332        0.3367
UK          0.8128        0.5136

Sensitivity - exclusively breastfed

Blue = seroconversion+, Orange = seroconversion-.

N by country

, ,  = IND (neo-), exclusively breastfed

   
    BS1 BS2 BS3 BS5
  0  82  82  83  76
  1  30  28  30  27

P values, longitudinal mixed-effects models

[1] 0.008352455

P values, cross-sectional models

  week      p
1    1 0.0176
2    4 0.0133
3    6 0.0768
4   10 0.9653

Sensitivity - vaginal delivery

Blue = seroconversion+, Orange = seroconversion-.

N by country

, ,  = IND (neo-), vaginal delivery

   
    BS1 BS2 BS3 BS5
  0  87  85  86  78
  1  22  21  24  23

P values, longitudinal mixed-effects models

[1] 0.004111159

P values, cross-sectional models

  week      p
1    1 0.0252
2    4 0.0087
3    6 0.0295
4   10 0.6119

Combined plot

Post-ORV RV-IgA

Week of life 1

Correlation coefficients values
                India India_exposed India_unexposed  Malawi     UK
Shannon       -0.0449       -0.0280         -0.1935  0.0002 0.0686
log(richness) -0.0991       -0.1125         -0.2388 -0.1469 0.0488
P values
               India India_exposed India_unexposed Malawi     UK
Shannon       0.4484        0.7290          0.0268 0.9986 0.6361
log(richness) 0.0939        0.1633          0.0060 0.2149 0.7365
N
  India India_neo_pos India_neo_neg Malawi UK
1   287           155           131     73 50
2   287           155           131     73 50

Week of life 4

Correlation coefficients values
                India India_exposed India_unexposed Malawi      UK
Shannon       -0.0464       -0.0616         -0.1852 0.0726 -0.0592
log(richness) -0.0421       -0.0218         -0.2700 0.1333 -0.0666
P values
               India India_exposed India_unexposed Malawi     UK
Shannon       0.4351        0.4451          0.0363 0.5475 0.6832
log(richness) 0.4785        0.7874          0.0021 0.2678 0.6460
N
  India India_neo_pos India_neo_neg Malawi UK
1   285           156           128     71 50
2   285           156           128     71 50

Week of life 6

Correlation coefficients values
                India India_exposed India_unexposed  Malawi      UK
Shannon       -0.0210        0.0787         -0.1729 -0.3348 -0.0384
log(richness) -0.0609        0.0529         -0.2138 -0.2894 -0.0911
P values
               India India_exposed India_unexposed Malawi     UK
Shannon       0.7228        0.3321          0.0474 0.0060 0.7958
log(richness) 0.3037        0.5147          0.0138 0.0184 0.5382
N
  India India_neo_pos India_neo_neg Malawi UK
1   287           154           132     66 48
2   287           154           132     66 48

Week of life 10

Correlation coefficients values
                India India_exposed India_unexposed  Malawi      UK
Shannon       -0.0469       -0.0433         -0.0427  0.0791 -0.0627
log(richness) -0.0409        0.0501         -0.0752 -0.0329 -0.0044
P values
               India India_exposed India_unexposed Malawi     UK
Shannon       0.4338        0.5870          0.6435 0.5736 0.6687
log(richness) 0.4942        0.5296          0.4144 0.8149 0.9761
N
  India India_neo_pos India_neo_neg Malawi UK
1   281           160           120     53 49
2   281           160           120     53 49

Dose 1 shedding

Longitudinal plots - Shannon

Longitudinal plots - richness

N by country

, ,  = IND

   
    BS1 BS2 BS3
  0 214 208 211
  1  73  77  76

, ,  = MLW

   
    BS1 BS2 BS3
  0  29  32  32
  1  39  32  25

, ,  = UK

   
    BS1 BS2 BS3
  0   0   0   0
  1   0   0   0

, ,  = IND (neo+)

   
    BS1 BS2 BS3
  0 127 126 126
  1  26  28  26

, ,  = IND (neo-)

   
    BS1 BS2 BS3
  0  85  80  83
  1  46  48  49

P values, cross-sectional analayses

See Module 5 for full univariate and multivariate analyses.

P values, longitudinal mixed-effects models

           Shannon log(Observed)
IND         0.1729        0.0868
IND (neo+)  0.8628        0.8004
IND (neo-)  0.2459        0.0458
MLW         0.2611        0.1195

Beta diversity

Column

Unweighted

Seroconversion

                    R2     p   n    country week full        outcome
IND_BS1      0.5500733 0.150 287        IND    1    1 seroconversion
IND_BS2      0.5250622 0.164 285        IND    4    1 seroconversion
IND_BS3      0.5030413 0.188 287        IND    6    1 seroconversion
IND_BS5      0.2309698 0.759 281        IND   10    1 seroconversion
MLW_BS1      2.9310572 0.022  73        MLW    1    1 seroconversion
MLW_BS2      1.4137453 0.441  71        MLW    4    1 seroconversion
MLW_BS3      3.5453057 0.025  66        MLW    6    1 seroconversion
MLW_BS5      3.4062591 0.053  53        MLW   10    1 seroconversion
UK_BS1       0.7134424 0.921  50         UK    1    1 seroconversion
UK_BS2       1.5371026 0.634  50         UK    4    1 seroconversion
UK_BS3       2.2358672 0.392  48         UK    6    1 seroconversion
UK_BS5       1.9618925 0.480  49         UK   10    1 seroconversion
INDexp_BS1   0.5738562 0.551 155 IND (neo+)    1    0 seroconversion
INDexp_BS2   0.2444851 0.919 156 IND (neo+)    4    0 seroconversion
INDexp_BS3   0.4977629 0.661 154 IND (neo+)    6    0 seroconversion
INDexp_BS5   0.3269280 0.846 160 IND (neo+)   10    0 seroconversion
INDunexp_BS1 1.7366233 0.042 131 IND (neo-)    1    0 seroconversion
INDunexp_BS2 1.7686967 0.029 128 IND (neo-)    4    0 seroconversion
INDunexp_BS3 1.2315230 0.118 132 IND (neo-)    6    0 seroconversion
INDunexp_BS5 1.6744514 0.035 120 IND (neo-)   10    0 seroconversion

RV-IgA

                    R2     p   n    country week full           outcome
IND_BS1      0.6292447 0.070 287        IND    1    1 RV-IgA (post-ORV)
IND_BS2      0.1980068 0.804 285        IND    4    1 RV-IgA (post-ORV)
IND_BS3      0.3024169 0.538 287        IND    6    1 RV-IgA (post-ORV)
IND_BS5      0.6028893 0.087 281        IND   10    1 RV-IgA (post-ORV)
MLW_BS1      2.2095504 0.107  73        MLW    1    1 RV-IgA (post-ORV)
MLW_BS2      1.6427758 0.318  71        MLW    4    1 RV-IgA (post-ORV)
MLW_BS3      3.3895945 0.028  66        MLW    6    1 RV-IgA (post-ORV)
MLW_BS5      2.1835129 0.326  53        MLW   10    1 RV-IgA (post-ORV)
UK_BS1       0.3264735 0.979  53         UK    1    1 RV-IgA (post-ORV)
UK_BS2       1.7483228 0.480  53         UK    4    1 RV-IgA (post-ORV)
UK_BS3       2.0692047 0.475  48         UK    6    1 RV-IgA (post-ORV)
UK_BS5       1.4369206 0.701  51         UK   10    1 RV-IgA (post-ORV)
INDexp_BS1   0.9153157 0.193 155 IND (neo+)    1    0 RV-IgA (post-ORV)
INDexp_BS2   0.2280854 0.916 156 IND (neo+)    4    0 RV-IgA (post-ORV)
INDexp_BS3   0.7483168 0.329 154 IND (neo+)    6    0 RV-IgA (post-ORV)
INDexp_BS5   0.8562789 0.214 160 IND (neo+)   10    0 RV-IgA (post-ORV)
INDunexp_BS1 2.0064704 0.011 131 IND (neo-)    1    0 RV-IgA (post-ORV)
INDunexp_BS2 1.1238038 0.190 128 IND (neo-)    4    0 RV-IgA (post-ORV)
INDunexp_BS3 1.2214353 0.114 132 IND (neo-)    6    0 RV-IgA (post-ORV)
INDunexp_BS5 1.5510248 0.056 120 IND (neo-)   10    0 RV-IgA (post-ORV)

Dose 1 shedding

                    R2     p   n    country week full         outcome
IND_BS1      0.3476460 0.462 287        IND    1    1 dose 1 shedding
IND_BS2      0.2577430 0.648 285        IND    4    1 dose 1 shedding
IND_BS3      0.3835346 0.359 287        IND    6    1 dose 1 shedding
MLW_BS1      1.3418396 0.500  68        MLW    1    1 dose 1 shedding
MLW_BS2      1.9160091 0.277  64        MLW    4    1 dose 1 shedding
MLW_BS3      1.5974604 0.522  57        MLW    6    1 dose 1 shedding
INDexp_BS1   0.1307968 0.980 153 IND (neo+)    1    0 dose 1 shedding
INDexp_BS2   0.8715548 0.234 154 IND (neo+)    4    0 dose 1 shedding
INDexp_BS3   0.7444585 0.363 152 IND (neo+)    6    0 dose 1 shedding
INDunexp_BS1 0.8410342 0.375 131 IND (neo-)    1    0 dose 1 shedding
INDunexp_BS2 0.7048742 0.540 128 IND (neo-)    4    0 dose 1 shedding
INDunexp_BS3 0.9000949 0.292 132 IND (neo-)    6    0 dose 1 shedding

Weighted

Seroconversion

                    R2     p   n    country week full        outcome
IND_BS1      0.1574865 0.844 287        IND    1    1 seroconversion
IND_BS2      0.9963383 0.017 285        IND    4    1 seroconversion
IND_BS3      0.2530616 0.600 287        IND    6    1 seroconversion
IND_BS5      0.2163289 0.746 281        IND   10    1 seroconversion
MLW_BS1      0.4422911 0.959  73        MLW    1    1 seroconversion
MLW_BS2      1.0286009 0.715  71        MLW    4    1 seroconversion
MLW_BS3      1.6270093 0.358  66        MLW    6    1 seroconversion
MLW_BS5      1.6183212 0.541  53        MLW   10    1 seroconversion
UK_BS1       0.5658089 0.973  50         UK    1    1 seroconversion
UK_BS2       1.0992741 0.813  50         UK    4    1 seroconversion
UK_BS3       2.7201641 0.251  48         UK    6    1 seroconversion
UK_BS5       1.1338328 0.816  49         UK   10    1 seroconversion
INDexp_BS1   0.4404823 0.704 155 IND (neo+)    1    0 seroconversion
INDexp_BS2   1.0807725 0.133 156 IND (neo+)    4    0 seroconversion
INDexp_BS3   0.7024854 0.334 154 IND (neo+)    6    0 seroconversion
INDexp_BS5   0.3730366 0.740 160 IND (neo+)   10    0 seroconversion
INDunexp_BS1 1.0616777 0.230 131 IND (neo-)    1    0 seroconversion
INDunexp_BS2 1.3730370 0.097 128 IND (neo-)    4    0 seroconversion
INDunexp_BS3 0.3989700 0.808 132 IND (neo-)    6    0 seroconversion
INDunexp_BS5 0.5170344 0.773 120 IND (neo-)   10    0 seroconversion

RV-IgA

                      R2     p   n    country week full           outcome
IND_BS1      0.259747270 0.591 287        IND    1    1 RV-IgA (post-ORV)
IND_BS2      0.235555444 0.624 285        IND    4    1 RV-IgA (post-ORV)
IND_BS3      0.187059649 0.789 287        IND    6    1 RV-IgA (post-ORV)
IND_BS5      0.250209280 0.689 281        IND   10    1 RV-IgA (post-ORV)
MLW_BS1      0.041350635 1.000  73        MLW    1    1 RV-IgA (post-ORV)
MLW_BS2      1.191293224 0.581  71        MLW    4    1 RV-IgA (post-ORV)
MLW_BS3      1.124968193 0.630  66        MLW    6    1 RV-IgA (post-ORV)
MLW_BS5      0.973253602 0.828  53        MLW   10    1 RV-IgA (post-ORV)
UK_BS1       0.563487140 0.961  53         UK    1    1 RV-IgA (post-ORV)
UK_BS2       1.613267269 0.562  53         UK    4    1 RV-IgA (post-ORV)
UK_BS3       1.847136338 0.535  48         UK    6    1 RV-IgA (post-ORV)
UK_BS5       0.270076162 0.995  51         UK   10    1 RV-IgA (post-ORV)
INDexp_BS1   0.003460839 0.997 155 IND (neo+)    1    0 RV-IgA (post-ORV)
INDexp_BS2   0.288201200 0.867 156 IND (neo+)    4    0 RV-IgA (post-ORV)
INDexp_BS3   0.927379883 0.204 154 IND (neo+)    6    0 RV-IgA (post-ORV)
INDexp_BS5   0.676041641 0.359 160 IND (neo+)   10    0 RV-IgA (post-ORV)
INDunexp_BS1 1.426836052 0.079 131 IND (neo-)    1    0 RV-IgA (post-ORV)
INDunexp_BS2 0.554642999 0.605 128 IND (neo-)    4    0 RV-IgA (post-ORV)
INDunexp_BS3 0.484489119 0.720 132 IND (neo-)    6    0 RV-IgA (post-ORV)
INDunexp_BS5 0.599110894 0.665 120 IND (neo-)   10    0 RV-IgA (post-ORV)

Dose 1 shedding

                    R2     p   n    country week full         outcome
IND_BS1      0.1417872 0.868 287        IND    1    1 dose 1 shedding
IND_BS2      0.2691645 0.596 285        IND    4    1 dose 1 shedding
IND_BS3      0.1646292 0.832 287        IND    6    1 dose 1 shedding
MLW_BS1      0.8147157 0.846  68        MLW    1    1 dose 1 shedding
MLW_BS2      3.0127436 0.062  64        MLW    4    1 dose 1 shedding
MLW_BS3      1.9326806 0.346  57        MLW    6    1 dose 1 shedding
INDexp_BS1   0.6874234 0.380 153 IND (neo+)    1    0 dose 1 shedding
INDexp_BS2   0.9430243 0.162 154 IND (neo+)    4    0 dose 1 shedding
INDexp_BS3   0.3845373 0.748 152 IND (neo+)    6    0 dose 1 shedding
INDunexp_BS1 1.0834230 0.203 131 IND (neo-)    1    0 dose 1 shedding
INDunexp_BS2 0.3971430 0.821 128 IND (neo-)    4    0 dose 1 shedding
INDunexp_BS3 0.7381359 0.435 132 IND (neo-)    6    0 dose 1 shedding

Differential taxa

Column

Seroconversion

Genus- and RSV-level models

Summary plot

Differential genera - Fisher’s test or Aldex2 (FDR p <0.05)

Differential RSVs - Fisher’s test or Aldex2 (FDR p <0.05)

RV-IgA

Genus- and RSV-level models

Summary plot

Differential genera - Fisher’s test or Aldex2 (FDR p <0.05)

Differential RSVs - Fisher’s test or Aldex2 (FDR p <0.05)

Dose 1 shedding

Genus- and RSV-level models

Summary plot

Differential genera - Fisher’s test or Aldex2 (FDR p <0.05)

Differential RSVs - Fisher’s test or Aldex2 (FDR p <0.05)

Summary figures

Seroconversion

RV-IgA

Dose 1 shedding

Longitudinal abundance comparisons

Immunogenicity

Number of infants/taxa included in longitudinal models:

  • India (full), n infants: 305; n samples: 1140; n taxa: 25
  • India (exposed), n infants: 166; n samples: 625; n taxa: 26
  • India (unexposed), n infants: 138; n samples: 511; n taxa: 24
  • Malawi, n infants: 96; n samples: 263; n taxa: 42
  • UK, n infants: 51; n samples: 197; n taxa: 25

India

          
           negatively correlated ns positively correlated
  age                          6 12                     7
  IgA                          0 25                     0
  seroconv                     0 25                     0
                         taxon Estimate Std.Error          padj comparison
1              Bifidobacterium    0.016     0.005  2.954545e-03        age
4               Staphylococcus   -0.495     0.011 1.700000e-218        age
6                  Veillonella    0.110     0.011  1.550000e-22        age
7                Lactobacillus    0.054     0.011  4.000000e-06        age
9                  Haemophilus   -0.186     0.011  2.666667e-55        age
10                  Klebsiella   -0.116     0.012  1.562500e-20        age
11                Enterococcus    0.029     0.012  2.884615e-02        age
13  unassigned_Lachnospiraceae   -0.114     0.012  5.714286e-21        age
14                     Gemella   -0.059     0.010  9.722222e-09        age
15                Enterobacter    0.034     0.011  3.541667e-03        age
18 Clostridium_sensu_stricto_1   -0.154     0.014  2.125000e-26        age
20                   Atopobium    0.250     0.010 7.625000e-108        age
21                 Actinomyces    0.080     0.008  6.666667e-22        age

Summary statistics

[1] "No significant differences according to ORV outcome"

India (exposed)

          
           negatively correlated ns positively correlated
  age                          7 11                     8
  IgA                          1 25                     0
  seroconv                     0 26                     0
                           taxon Estimate Std.Error          padj comparison
1                Bifidobacterium    0.020     0.007  6.145455e-03        age
4                 Staphylococcus   -0.465     0.016 9.880000e-108        age
6                    Veillonella    0.107     0.015  8.450000e-12        age
7                  Lactobacillus    0.057     0.013  2.892500e-05        age
9                    Haemophilus   -0.076     0.015  9.966667e-07        age
10                    Klebsiella   -0.080     0.016  3.380000e-06        age
12                        Rothia    0.039     0.014  1.040000e-02        age
13    unassigned_Lachnospiraceae   -0.050     0.017  7.800000e-03        age
14                       Gemella   -0.048     0.013  6.355556e-04        age
18   Clostridium_sensu_stricto_1   -0.121     0.018  3.172000e-10        age
19 unassigned_Enterobacteriaceae    0.036     0.014  2.228571e-02        age
20                Clostridioides   -0.054     0.015  1.040000e-03        age
21                     Atopobium    0.241     0.013  8.710000e-57        age
22                   Actinomyces    0.147     0.013  3.380000e-24        age
23                    Finegoldia    0.100     0.044  3.813333e-02        age
59                 Lactobacillus   -0.181     0.055  3.640000e-02        IgA

Summary statistics

           taxon Estimate Std.Error   padj comparison  mean prev
59 Lactobacillus   -0.181     0.055 0.0364        IgA 3.685 62.7

India (unexposed)

          
           negatively correlated ns positively correlated
  age                          6 10                     8
  IgA                          0 24                     0
  seroconv                     0 24                     0
                         taxon Estimate Std.Error          padj comparison
4               Staphylococcus   -0.531     0.016 1.200000e-112        age
6                  Veillonella    0.127     0.016  2.948571e-14        age
7                Lactobacillus    0.049     0.017  6.000000e-03        age
8                  Collinsella    0.047     0.015  3.138462e-03        age
9                  Haemophilus   -0.284     0.016  1.560000e-51        age
10                  Klebsiella   -0.166     0.018  7.200000e-18        age
11                Enterococcus    0.112     0.018  1.333333e-09        age
13  unassigned_Lachnospiraceae   -0.168     0.014  2.480000e-26        age
14                     Gemella   -0.066     0.015  4.000000e-05        age
15                Enterobacter    0.073     0.015  2.880000e-06        age
16               Acinetobacter    0.089     0.014  6.900000e-10        age
18 Clostridium_sensu_stricto_1   -0.218     0.021  1.632000e-22        age
19                   Atopobium    0.203     0.018  1.680000e-25        age
24               Peptoniphilus    0.065     0.014  4.363636e-06        age

Summary statistics

[1] "No significant differences according to ORV outcome"

Malawi

          
           negatively correlated ns positively correlated
  age                         11 16                    15
  IgA                          0 42                     0
  seroconv                     0 42                     0
                          taxon Estimate Std.Error         padj comparison
1               Bifidobacterium    0.068     0.019 1.085000e-03        age
4                Staphylococcus   -0.435     0.026 1.134000e-36        age
5                   Bacteroides    0.068     0.019 1.085000e-03        age
7                 Lactobacillus    0.103     0.028 7.400000e-04        age
8                   Collinsella   -0.213     0.026 1.565455e-13        age
9                   Haemophilus   -0.148     0.023 2.001176e-09        age
10                   Klebsiella   -0.245     0.027 1.680000e-15        age
12                       Rothia    0.181     0.024 1.995000e-11        age
13   unassigned_Lachnospiraceae   -0.088     0.023 4.830000e-04        age
18                 Enterobacter   -0.390     0.037 2.280000e-19        age
21                Enhydrobacter    0.190     0.022 5.460000e-14        age
23  Clostridium_sensu_stricto_1   -0.160     0.024 1.443750e-09        age
24        Phascolarctobacterium   -0.100     0.030 1.848000e-03        age
25                Succinivibrio   -0.613     0.019 8.820000e-72        age
26                   Sutterella   -0.168     0.025 3.920000e-10        age
29                 Holdemanella    0.093     0.026 8.209091e-04        age
30                      Slackia    0.069     0.022 2.746154e-03        age
31             Senegalimassilia    0.128     0.022 9.947368e-08        age
32                    Atopobium    0.347     0.022 3.864000e-33        age
33                  Actinomyces    0.131     0.023 7.466667e-08        age
34                   Lawsonella    0.387     0.022 1.533000e-38        age
35                   Finegoldia    0.179     0.021 2.566667e-14        age
36                    Ezakiella    0.128     0.018 1.098462e-10        age
39 unassigned_Saccharimonadales   -0.309     0.020 3.780000e-33        age
41                   Prevotella    0.169     0.024 1.740000e-10        age
42                Peptoniphilus    0.337     0.022 6.230000e-32        age

Summary statistics

[1] "No significant differences according to ORV outcome"

UK

          
           negatively correlated ns positively correlated
  age                         11 10                     4
  IgA                          0 24                     0
  seroconv                     0 25                     0
                  taxon Estimate Std.Error         padj comparison
2  Escherichia/Shigella    0.045     0.013 1.750000e-03        age
3         Streptococcus   -0.119     0.024 5.312500e-06        age
4        Staphylococcus   -0.435     0.025 1.825000e-35        age
9           Haemophilus   -0.247     0.024 2.625000e-18        age
10           Klebsiella   -0.156     0.020 3.125000e-12        age
11         Enterococcus   -0.115     0.024 1.305556e-05        age
14              Gemella   -0.120     0.020 3.214286e-08        age
15         Enterobacter   -0.050     0.017 6.964286e-03        age
16      Parabacteroides   -0.051     0.016 2.500000e-03        age
17    Corynebacterium_1   -0.164     0.023 1.625000e-10        age
20       Granulicatella   -0.063     0.015 1.225000e-04        age
22          Actinomyces   -0.234     0.032 5.500000e-11        age
23          Eggerthella    0.146     0.018 1.916667e-12        age
24       Negativicoccus    0.058     0.021 1.016667e-02        age
25           Prevotella    0.256     0.078 2.500000e-03        age

Summary statistics

[1] "No significant differences according to ORV outcome"

Dose 1 shedding

Number of infants/taxa included in longitudinal models:

  • India (full), n infants: 305; n samples: 859; n taxa: 23
  • India (exposed), n infants: 164; n samples: 459; n taxa: 24
  • India (unexposed), n infants: 138; n samples: 391; n taxa: 22
  • Malawi, n infants: 89; n samples: 189; n taxa: 44
  • UK, n infants: 60; n samples: 171; n taxa: 21

India

       
        ns
  dose1 23

Summary statistics

[1] "No significant differences according to ORV outcome"

India (exposed)

       
        ns
  dose1 24

Summary statistics

[1] "No significant differences according to ORV outcome"

India (unexposed)

       
        ns
  dose1 22

Summary statistics

[1] "No significant differences according to ORV outcome"

Malawi

       
        negatively correlated ns
  dose1                     1 42

Summary statistics

        taxon Estimate Std.Error    padj comparison mean prev
28 Sutterella   -1.417     0.369 0.01032      dose1 1.28 43.9

.

Session info

R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] FSA_0.9.3                   ALDEx2_1.26.0              
 [3] zCompositions_1.4.0-1       truncnorm_1.0-8            
 [5] NADA_1.6-1.1                survival_3.2-13            
 [7] MASS_7.3-55                 sjstats_0.18.1             
 [9] ggExtra_0.10.0              formattable_0.2.1          
[11] NBZIMM_1.0                  inlmisc_0.5.5              
[13] decontam_1.14.0             ggtree_3.2.1               
[15] wesanderson_0.3.6           phangorn_2.8.1             
[17] ape_5.6-1                   DECIPHER_2.22.0            
[19] RSQLite_2.2.12              Biostrings_2.62.0          
[21] XVector_0.34.0              cowplot_1.1.1              
[23] scales_1.1.1                RVAideMemoire_0.9-81-2     
[25] DescTools_0.99.44           ggsignif_0.6.3             
[27] binom_1.1-1                 shiny_1.7.1                
[29] randomcoloR_1.1.0.1         DESeq2_1.34.0              
[31] SummarizedExperiment_1.24.0 Biobase_2.54.0             
[33] MatrixGenerics_1.6.0        GenomicRanges_1.46.1       
[35] GenomeInfoDb_1.30.1         IRanges_2.28.0             
[37] S4Vectors_0.32.3            BiocGenerics_0.40.0        
[39] crossval_1.0.4              UpSetR_1.4.0               
[41] labdsv_2.0-1                mgcv_1.8-38                
[43] nlme_3.1-155                ggpubr_0.4.0               
[45] data.table_1.14.2           corrplot_0.92              
[47] ZIBR_0.1                    vegan_2.5-7                
[49] lattice_0.20-45             permute_0.9-7              
[51] randomForest_4.7-1          matrixStats_0.61.0         
[53] lme4_1.1-28                 Matrix_1.4-0               
[55] reshape2_1.4.4              pheatmap_1.0.12            
[57] DT_0.21                     plotly_4.10.0              
[59] cluster_2.1.2               tidyr_1.2.0                
[61] dplyr_1.0.8                 magrittr_2.0.2             
[63] plyr_1.8.6                  kableExtra_1.3.4           
[65] gridExtra_2.3               RColorBrewer_1.1-2         
[67] knitr_1.37                  ggplot2_3.3.5              
[69] phyloseq_1.38.0            

loaded via a namespace (and not attached):
  [1] estimability_1.3       coda_0.19-4            bit64_4.0.5           
  [4] DelayedArray_0.20.0    KEGGREST_1.34.0        RCurl_1.98-1.6        
  [7] generics_0.1.2         terra_1.5-17           proxy_0.4-26          
 [10] bit_4.0.4              webshot_0.5.2          xml2_1.3.3            
 [13] httpuv_1.6.5           assertthat_0.2.1       xfun_0.29             
 [16] jquerylib_0.1.4        evaluate_0.14          promises_1.2.0.1      
 [19] fansi_1.0.2            igraph_1.2.11          DBI_1.1.2             
 [22] geneplotter_1.72.0     htmlwidgets_1.5.4      purrr_0.3.4           
 [25] ellipsis_0.3.2         backports_1.4.1        V8_4.1.0              
 [28] insight_0.17.0         annotate_1.72.0        vctrs_0.3.8           
 [31] sjlabelled_1.1.8       abind_1.4-5            cachem_1.0.6          
 [34] withr_2.4.3            rgdal_1.5-28           emmeans_1.7.3         
 [37] treeio_1.18.1          svglite_2.1.0          lazyeval_0.2.2        
 [40] crayon_1.4.2           flexdashboard_0.5.2    genefilter_1.76.0     
 [43] labeling_0.4.2         pkgconfig_2.0.3        rlang_1.0.1           
 [46] lifecycle_1.0.1        miniUI_0.1.1.1         modelr_0.1.8          
 [49] datawizard_0.4.0       aplot_0.1.6            raster_3.5-15         
 [52] carData_3.0-5          Rhdf5lib_1.16.0        boot_1.3-28           
 [55] png_0.1-7              viridisLite_0.4.0      parameters_0.17.0     
 [58] rootSolve_1.8.2.3      bitops_1.0-7           rhdf5filters_1.6.0    
 [61] blob_1.2.2             stringr_1.4.0          rstatix_0.7.0         
 [64] gridGraphics_0.5-1     memoise_2.0.1          zlibbioc_1.40.0       
 [67] compiler_4.1.2         cli_3.1.1              ade4_1.7-18           
 [70] patchwork_1.1.1        tidyselect_1.1.1       stringi_1.7.6         
 [73] highr_0.9              yaml_2.2.2             locfit_1.5-9.5        
 [76] grid_4.1.2             sass_0.4.0             fastmatch_1.1-3       
 [79] tools_4.1.2            lmom_2.8               rstudioapi_0.13       
 [82] foreach_1.5.2          gld_2.6.4              farver_2.1.0          
 [85] Rtsne_0.15             RcppZiggurat_0.1.6     digest_0.6.29         
 [88] quadprog_1.5-8         Rcpp_1.0.8             car_3.0-12            
 [91] broom_0.7.12           performance_0.9.0      later_1.3.0           
 [94] httr_1.4.2             AnnotationDbi_1.56.2   effectsize_0.6.0.1    
 [97] colorspace_2.0-2       rvest_1.0.2            XML_3.99-0.10         
[100] splines_4.1.2          yulab.utils_0.0.5      tidytree_0.3.9        
[103] expm_0.999-6           sp_1.4-6               multtest_2.50.0       
[106] Exact_3.1              ggplotify_0.1.0        systemfonts_1.0.4     
[109] xtable_1.8-4           jsonlite_1.7.3         nloptr_2.0.0          
[112] Rfast_2.0.6            ggfun_0.0.6            R6_2.5.1              
[115] pillar_1.7.0           htmltools_0.5.2        mime_0.12             
[118] glue_1.6.1             fastmap_1.1.0          minqa_1.2.4           
[121] BiocParallel_1.28.3    class_7.3-20           codetools_0.2-18      
[124] mvtnorm_1.1-3          utf8_1.2.2             bslib_0.3.1           
[127] tibble_3.1.6           curl_4.3.2             rmarkdown_2.11        
[130] biomformat_1.22.0      munsell_0.5.0          e1071_1.7-9           
[133] rhdf5_2.38.0           GenomeInfoDbData_1.2.7 iterators_1.0.14      
[136] sjmisc_2.8.9           gtable_0.3.0           bayestestR_0.11.5     

.